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#ifndef SHHHSEQSCOMMAND_H
#define SHHHSEQSCOMMAND_H
/*
* shhhseqscommand.h
* Mothur
*
* Created by westcott on 11/8/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "myseqdist.h"
#include "seqnoise.h"
#include "sequenceparser.h"
#include "deconvolutecommand.h"
#include "clustercommand.h"
//**********************************************************************************************************************
class ShhhSeqsCommand : public Command {
public:
ShhhSeqsCommand(string);
ShhhSeqsCommand();
~ShhhSeqsCommand() {}
vector<string> setParameters();
string getCommandName() { return "shhh.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nhttp://www.mothur.org/wiki/Shhh.seqs"; }
string getDescription() { return "shhh.seqs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
struct linePair {
int start;
int end;
linePair(int i, int j) : start(i), end(j) {}
};
bool abort;
string outputDir, fastafile, namefile, groupfile;
int processors;
double sigma;
vector<string> outputNames;
int readData(correctDist*, seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&);
int loadData(correctDist*, seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&, map<string, string>&, vector<Sequence>&);
int driver(seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&, string, string, string, string);
vector<string> driverGroups(SequenceParser&, string, string, string, int, int, vector<string>);
vector<string> createProcessesGroups(SequenceParser&, string, string, string, vector<string>);
int deconvoluteResults(string, string);
};
/**************************************************************************************************/
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct shhhseqsData {
string fastafile;
string namefile;
string groupfile;
string newFName, newNName, newMName;
MothurOut* m;
int start;
int end;
int sigma, threadID, count;
vector<string> groups;
vector<string> mapfileNames;
shhhseqsData(){}
shhhseqsData(string f, string n, string g, string nff, string nnf, string nmf, vector<string> gr, MothurOut* mout, int st, int en, int s, int tid) {
fastafile = f;
namefile = n;
groupfile = g;
newFName = nff;
newNName = nnf;
newMName = nmf;
m = mout;
start = st;
end = en;
sigma = s;
threadID = tid;
groups = gr;
count=0;
}
};
/**************************************************************************************************/
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
shhhseqsData* pDataArray;
pDataArray = (shhhseqsData*)lpParam;
try {
//parse fasta and name file by group
SequenceParser parser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);
//precluster each group
for (int k = pDataArray->start; k < pDataArray->end; k++) {
pDataArray->count++;
int start = time(NULL);
if (pDataArray->m->control_pressed) { return 0; }
pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Processing group " + pDataArray->groups[k] + ":"); pDataArray->m->mothurOutEndLine();
map<string, string> thisNameMap;
thisNameMap = parser.getNameMap(pDataArray->groups[k]);
vector<Sequence> thisSeqs = parser.getSeqs(pDataArray->groups[k]);
if (pDataArray->m->control_pressed) { return 0; }
vector<string> sequences;
vector<string> uniqueNames;
vector<string> redundantNames;
vector<int> seqFreq;
seqNoise noise;
correctDist* correct = new correctDist(1); //we use one processor since we already split up the work load.
//load this groups info in order
//loadData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq, thisNameMap, thisSeqs);
//////////////////////////////////////////////////////////////////////////////////////////////////
bool error = false;
map<string, string>::iterator it;
for (int i = 0; i < thisSeqs.size(); i++) {
if (pDataArray->m->control_pressed) { return 0; }
if (thisSeqs[i].getName() != "") {
correct->addSeq(thisSeqs[i].getName(), thisSeqs[i].getAligned());
it = thisNameMap.find(thisSeqs[i].getName());
if (it != thisNameMap.end()) {
noise.addSeq(thisSeqs[i].getAligned(), sequences);
noise.addRedundantName(it->first, it->second, uniqueNames, redundantNames, seqFreq);
}else {
pDataArray->m->mothurOut("[ERROR]: " + thisSeqs[i].getName() + " is in your fasta file and not in your namefile, please correct.");
error = true;
}
}
}
if (error) { return 0; }
//////////////////////////////////////////////////////////////////////////////////////////////////
if (pDataArray->m->control_pressed) { return 0; }
//calc distances for cluster
string distFileName = pDataArray->m->getRootName(pDataArray->m->getSimpleName(pDataArray->fastafile)) + pDataArray->groups[k] + ".shhh.dist";
correct->execute(distFileName);
delete correct;
if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(distFileName); return 0; }
//driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, newFFile+groups[i], newNFile+groups[i], newMFile+groups[i]+".map");
///////////////////////////////////////////////////////////////////////////////////////////////////
double cutOff = 0.08;
int minIter = 10;
int maxIter = 1000;
double minDelta = 1e-6;
int numIters = 0;
double maxDelta = 1e6;
int numSeqs = sequences.size();
//run cluster command
string inputString = "phylip=" + distFileName + ", method=furthest, cutoff=0.08";
pDataArray->m->mothurOut("/******************************************/"); pDataArray->m->mothurOutEndLine();
pDataArray->m->mothurOut("Running command: cluster(" + inputString + ")"); pDataArray->m->mothurOutEndLine();
Command* clusterCommand = new ClusterCommand(inputString);
clusterCommand->execute();
map<string, vector<string> > filenames = clusterCommand->getOutputFiles();
string listFileName = filenames["list"][0];
string rabundFileName = filenames["rabund"][0]; pDataArray->m->mothurRemove(rabundFileName);
string sabundFileName = filenames["sabund"][0]; pDataArray->m->mothurRemove(sabundFileName);
delete clusterCommand;
pDataArray->m->mothurOut("/******************************************/"); pDataArray->m->mothurOutEndLine();
if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(distFileName); pDataArray->m->mothurRemove(listFileName); return 0; }
vector<double> distances(numSeqs * numSeqs);
noise.getDistanceData(distFileName, distances);
pDataArray->m->mothurRemove(distFileName);
if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(listFileName); return 0; }
vector<int> otuData(numSeqs);
vector<int> otuFreq;
vector<vector<int> > otuBySeqLookUp;
noise.getListData(listFileName, cutOff, otuData, otuFreq, otuBySeqLookUp);
pDataArray->m->mothurRemove(listFileName);
if (pDataArray->m->control_pressed) { return 0; }
int numOTUs = otuFreq.size();
vector<double> weights(numOTUs, 0);
vector<int> change(numOTUs, 1);
vector<int> centroids(numOTUs, -1);
vector<int> cumCount(numOTUs, 0);
vector<double> tau(numSeqs, 1);
vector<int> anP(numSeqs, 0);
vector<int> anI(numSeqs, 0);
vector<int> anN(numSeqs, 0);
vector<vector<int> > aanI = otuBySeqLookUp;
while(numIters < minIter || ((maxDelta > minDelta) && (numIters < maxIter))){
if (pDataArray->m->control_pressed) { return 0; }
noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (pDataArray->m->control_pressed) { return 0; }
maxDelta = noise.calcNewWeights(weights, seqFreq, anI, cumCount, anP, otuFreq, tau); if (pDataArray->m->control_pressed) { return 0; }
noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (pDataArray->m->control_pressed) { return 0; }
noise.checkCentroids(weights, centroids); if (pDataArray->m->control_pressed) { return 0; }
otuFreq.assign(numOTUs, 0);
int total = 0;
for(int i=0;i<numSeqs;i++){
if (pDataArray->m->control_pressed) { return 0; }
double offset = 1e6;
double norm = 0.0000;
double minWeight = 0.1;
vector<double> currentTau(numOTUs);
for(int j=0;j<numOTUs;j++){
if (pDataArray->m->control_pressed) { return 0; }
if(weights[j] > minWeight && distances[i * numSeqs+centroids[j]] < offset){
offset = distances[i * numSeqs+centroids[j]];
}
}
for(int j=0;j<numOTUs;j++){
if (pDataArray->m->control_pressed) { return 0; }
if(weights[j] > minWeight){
currentTau[j] = exp(pDataArray->sigma * (-distances[(i * numSeqs + centroids[j])] + offset)) * weights[j];
norm += currentTau[j];
}
else{
currentTau[j] = 0.0000;
}
}
for(int j=0;j<numOTUs;j++){
if (pDataArray->m->control_pressed) { return 0; }
currentTau[j] /= norm;
}
for(int j=0;j<numOTUs;j++){
if (pDataArray->m->control_pressed) { return 0; }
if(currentTau[j] > 1.0e-4){
int oldTotal = total;
total++;
tau.resize(oldTotal+1);
tau[oldTotal] = currentTau[j];
otuBySeqLookUp[j][otuFreq[j]] = oldTotal;
aanI[j][otuFreq[j]] = i;
otuFreq[j]++;
}
}
anP.resize(total);
anI.resize(total);
}
numIters++;
}
noise.updateOTUCountData(otuFreq, otuBySeqLookUp, aanI, anP, anI, cumCount); if (pDataArray->m->control_pressed) { return 0; }
vector<double> percentage(numSeqs);
noise.setUpOTUData(otuData, percentage, cumCount, tau, otuFreq, anP, anI); if (pDataArray->m->control_pressed) { return 0; }
noise.finishOTUData(otuData, otuFreq, anP, anI, cumCount, otuBySeqLookUp, aanI, tau); if (pDataArray->m->control_pressed) { return 0; }
change.assign(numOTUs, 1);
noise.calcCentroids(anI, anP, change, centroids, cumCount, distances, seqFreq, otuFreq, tau); if (pDataArray->m->control_pressed) { return 0; }
vector<int> finalTau(numOTUs, 0);
for(int i=0;i<numSeqs;i++){
if (pDataArray->m->control_pressed) { return 0; }
finalTau[otuData[i]] += int(seqFreq[i]);
}
noise.writeOutput(pDataArray->newFName+pDataArray->groups[k], pDataArray->newNName+pDataArray->groups[k], pDataArray->newMName+pDataArray->groups[k]+".map", finalTau, centroids, otuData, sequences, uniqueNames, redundantNames, seqFreq, distances);
///////////////////////////////////////////////////////////////////////////////////////////////////
if (pDataArray->m->control_pressed) { return 0; }
pDataArray->m->appendFiles(pDataArray->newFName+pDataArray->groups[k], pDataArray->newFName); pDataArray->m->mothurRemove(pDataArray->newFName+pDataArray->groups[k]);
pDataArray->m->appendFiles(pDataArray->newNName+pDataArray->groups[k], pDataArray->newNName); pDataArray->m->mothurRemove(pDataArray->newNName+pDataArray->groups[k]);
pDataArray->mapfileNames.push_back(pDataArray->newMName+pDataArray->groups[k]+".map");
pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + pDataArray->groups[k] + "."); pDataArray->m->mothurOutEndLine();
}
return 0;
}
catch(exception& e) {
pDataArray->m->errorOut(e, "ShhhSeqsCommand", "MyShhhSeqsThreadFunction");
exit(1);
}
}
#endif
/**************************************************************************************************/
#endif
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